JezK

Edit File: workspace.php

<?php
$pageTitle = 'Research Workspace';
$extraCss = '
<link rel="stylesheet" href="css/workspace.css">
<style>
.document-list-sidebar{width:220px;border-right:1px solid var(--color-border);background:#fff;display:flex;flex-direction:column;}
.doc-item{padding:.75rem 1rem;font-size:.875rem;cursor:pointer;border-bottom:1px solid var(--color-border-subtle);display:flex;align-items:center;justify-content:space-between;gap:.5rem;}
.doc-item:hover,.doc-item.active{background:var(--primary-50);color:var(--primary-700);font-weight:600;}
</style>
';

include 'includes/header.php';
?>

<div class="main-area">
  <header class="topbar">
    <div class="topbar-title" id="workspace-project-title">Loading Workspace...</div>
    <div class="topbar-actions">
      <div class="badge badge-purple" style="display:inline-flex;align-items:center;gap:6px;padding:5px 12px;font-size:0.75rem;border:1px solid rgba(168,85,247,0.3);background:rgba(237,233,254,0.7);">
        <span class="live-dot" style="width:7px;height:7px;border-radius:50%;background:#10B981;box-shadow:0 0 8px #10B981;"></span>
        <span style="font-weight:700;color:var(--purple-700);">OX Alpha (Stealth) Engine</span>
      </div>
      <select class="select" id="workspace-style-select" style="width:auto;padding:.4rem .75rem;font-size:.8125rem;">
        <option>APA</option><option>MLA</option><option>Harvard</option>
        <option>Chicago</option><option>IEEE</option><option>Vancouver</option>
      </select>
      <button class="btn btn-secondary btn-sm" onclick="openVersionsDrawer()"><i data-lucide="history" style="width:14px;height:14px;"></i> Version History</button>
      <button class="btn btn-gradient btn-sm" onclick="triggerFullAnalysis()"><i data-lucide="shield-check" style="width:14px;height:14px;"></i> Run AI Integrity Check</button>
    </div>
  </header>

<div class="workspace-container">
    
    <div class="document-list-sidebar">
      <div style="padding:1rem;border-bottom:1px solid var(--color-border);display:flex;justify-content:space-between;align-items:center;">
        <strong style="font-size:.8rem;color:var(--gray-500)">DOCUMENTS</strong>
        <button class="btn btn-secondary btn-icon-sm" onclick="createNewDocument()" title="New Draft">+</button>
      </div>
      <div id="document-sidebar-list" style="flex:1;overflow-y:auto;">
        
      </div>
    </div>

<div class="editor-area">
      
      <div class="editor-toolbar" id="editor-toolbar">
        <div class="toolbar-group">
          <button class="toolbar-btn btn-bold" title="Bold"><b>B</b></button>
          <button class="toolbar-btn btn-italic" title="Italic"><i>I</i></button>
          <button class="toolbar-btn btn-underline" title="Underline"><u>U</u></button>
        </div>
        <div class="toolbar-group">
          <select class="toolbar-select" data-cmd="formatBlock">
            <option value="p">Paragraph</option>
            <option value="h1">Heading 1</option>
            <option value="h2">Heading 2</option>
            <option value="h3">Heading 3</option>
          </select>
        </div>
        <div class="toolbar-group">
          <button class="toolbar-btn btn-ul" title="Unordered List">•=</button>
          <button class="toolbar-btn btn-ol" title="Ordered List">1=</button>
        </div>
        <div class="toolbar-group">
          <button class="toolbar-btn btn-align-left" title="Align Left">←</button>
          <button class="toolbar-btn btn-align-center" title="Align Center">↔</button>
          <button class="toolbar-btn btn-align-right" title="Align Right">→</button>
        </div>
        <div class="toolbar-group">
          <button class="toolbar-btn btn-quote" title="Quote">”</button>
          <button class="toolbar-btn" data-cmd="createLink" title="Insert Link" style="display:flex;align-items:center;justify-content:center;"><i data-lucide="link" style="width:14px;height:14px;"></i></button>
        </div>
        <div class="toolbar-group">
          <button class="toolbar-btn" data-cmd="undo" title="Undo">↶</button>
          <button class="toolbar-btn" data-cmd="redo" title="Redo">↷</button>
        </div>
      </div>

<div class="editor-info-bar">
        <div class="save-indicator saved" id="save-indicator">
          <span class="live-dot" id="live-analysis-dot"></span>
          <span id="live-analysis-label">Writing protected by AI</span>
        </div>
        <div style="margin-left:auto;display:flex;gap:1rem;">
          <span class="word-count">0 words</span>
          <span class="char-count">0 characters</span>
        </div>
      </div>

<div class="editor-scroll">
        <div class="editor-page">
          <div class="editor-content" id="editor-content" placeholder="Start writing your research paper here...">
            <h1>CRISPR Mechanisms in Neurodegeneration - Draft 1</h1>
            <p>Alzheimer's disease (AD) represents one of the most devastating neurodegenerative disorders, affecting over 55 million individuals worldwide. The amyloid cascade hypothesis posits that the accumulation of beta-amyloid plaques initiates a pathological cascade leading to neuronal death.</p>
            <p>Recent advances in CRISPR-Cas9 technology have opened new therapeutic avenues for genetic diseases previously considered untreatable. The precision of guide RNA targeting allows researchers to edit specific genomic loci with unprecedented accuracy.</p>
            <h2>Methods</h2>
            <p>We employed a murine model expressing humanized APP and PSEN1 mutations. CRISPR editing was performed using AAV9 delivery vectors injected intracerebroventricularly.</p>
          </div>
        </div>
      </div>
    </div>

<div class="intel-panel">
      <div class="intel-panel-header">
        <div class="intel-panel-title"><i data-lucide="shield" style="width:16px;height:16px;color:var(--primary-600);"></i> Citation Intelligence</div>
        <div class="intel-tabs">
          <button class="intel-tab active" data-tab="alerts" onclick="switchIntelTab('alerts')">Alerts <span class="count" id="alerts-count">0</span></button>
          <button class="intel-tab" data-tab="suggestions" onclick="switchIntelTab('suggestions')">Sources</button>
          <button class="intel-tab" data-tab="similarity" onclick="switchIntelTab('similarity')">Similarity</button>
          <button class="intel-tab" data-tab="ai-verify" onclick="switchIntelTab('ai-verify')">AI Verify</button>
          <button class="intel-tab" data-tab="dna" onclick="switchIntelTab('dna')">DNA Profile</button>
        </div>
      </div>

<div class="intel-body">
        
        <div class="intel-pane active" id="pane-alerts">
          <div id="alerts-list">
            <div class="empty-state">
              <div class="empty-icon"><i data-lucide="check" style="width:24px;height:24px;color:var(--success-500);"></i></div>
              <div class="empty-title">All Statements Cited</div>
              <div class="empty-desc">No missing citation warnings detected in the current text scope.</div>
            </div>
          </div>
        </div>

<div class="intel-pane" id="pane-suggestions">
          <div style="display:flex;flex-direction:column;gap:.5rem;margin-bottom:1rem;">
            <div style="display:flex;gap:.25rem;">
              <select class="select input-sm" id="source-search-index" style="width:105px;padding:.25rem;font-size:10px;background:#fff;border:1px solid var(--color-border);" onchange="updateGoogleScholarLink()">
                <option value="local">Local Library</option>
                <option value="crossref">CrossRef</option>
                <option value="semantic">Semantic Scholar</option>
                <option value="pubmed">PubMed</option>
                <option value="arxiv">arXiv</option>
              </select>
              <input type="text" class="input input-sm" id="source-search-input" placeholder="Search..." onkeydown="if(event.key==='Enter') searchSources(this.value)" style="flex:1;min-width:0;">
              <button class="btn btn-primary btn-sm" onclick="searchSources(document.getElementById('source-search-input').value)" style="padding:.25rem .5rem;display:flex;align-items:center;justify-content:center;"><i data-lucide="search" style="width:12px;height:12px;"></i></button>
            </div>
            <div id="google-scholar-link-container" style="display:none;text-align:right;">
              <a href="#" id="google-scholar-link" target="_blank" class="text-xs text-primary font-semibold" style="display:inline-flex;align-items:center;gap:4px;">
                <i data-lucide="globe" style="width:12px;height:12px;"></i> Search Google Scholar
              </a>
            </div>
          </div>
          <div id="suggestions-list" style="max-height:calc(100vh - 280px);overflow-y:auto;padding-right:4px;">
            <p class="text-muted text-sm text-center">Suggestions will appear here based on selected statements.</p>
          </div>
        </div>

<div class="intel-pane" id="pane-similarity">
          <div style="display:flex;justify-content:space-between;margin-bottom:1rem;align-items:center;">
            <span class="text-sm font-semibold">Semantic Plagiarism Risk</span>
            <span class="badge risk-low" id="similarity-overall-badge">Low Risk</span>
          </div>
          <div style="margin-bottom:1.5rem;text-align:center;">
            <div style="font-size:2.5rem;font-weight:900;" id="similarity-score-text">0%</div>
            <div class="text-xs text-muted">Embedding Similarity Match</div>
          </div>
          <button class="btn btn-secondary btn-sm" style="width:100%;margin-bottom:1rem;" onclick="scanEntireDocSimilarity()">Scan Document for Plagiarism</button>
          <div id="similarity-list">
            <p class="text-muted text-sm text-center">Highlight sentences or click the button above to run plagiarism checks.</p>
          </div>
        </div>

<div class="intel-pane" id="pane-ai-verify">
          <div class="card" style="padding:1rem;margin-bottom:1rem;">
            <h4 style="margin-bottom:.5rem;">AI Text Detector</h4>
            <p class="text-xs text-muted" style="margin-bottom:1rem;">Evaluate potential AI-generated claims and verify citations presence.</p>
            <div style="display:flex;justify-content:space-between;align-items:center;margin-bottom:.5rem;">
              <span class="text-sm">Verification Score</span>
              <span class="badge badge-green" id="ai-verify-score">96/100</span>
            </div>
            <div style="display:flex;justify-content:space-between;align-items:center;margin-bottom:.5rem;">
              <span class="text-sm">AI Content Match</span>
              <span class="badge badge-blue" id="ai-content-score">4%</span>
            </div>
            <button class="btn btn-secondary btn-sm" style="width:100%;margin-top:.5rem;" onclick="checkAIContent()">Scan Entire Document</button>
          </div>
          <div id="ai-verify-details"></div>
        </div>

<div class="intel-pane" id="pane-dna">
          <div class="card" style="padding:1rem;margin-bottom:1rem;background:linear-gradient(135deg,#EFF6FF,#EDE9FE)">
            <h4 style="margin-bottom:.25rem;">Paragraph DNA Profile</h4>
            <p class="text-xs text-muted">Visual tracking of sources and origin integrity for every block of text.</p>
            <div style="font-size:2rem;font-weight:900;color:var(--primary-700);margin:1rem 0;" id="dna-overall-score">95%</div>
            <div class="text-xs font-semibold" id="dna-profile-type">INTEGRAL SOURCE ALIGNMENT</div>
          </div>
          <div id="dna-lineage-list">
            
          </div>
        </div>
      </div>

<div class="workspace-statusbar">
        <div class="statusbar-item good">Score: <span id="status-coverage-score">84%</span></div>
        <div class="statusbar-item warning">Risk: <span id="status-risk-score">12%</span></div>
        <div class="statusbar-item">Style: <span id="status-style">APA</span></div>
      </div>
    </div>
  </div>
</div>

<div class="modal-overlay" id="versions-drawer" style="justify-content:flex-end;padding:0;">
  <div class="modal" style="height:100vh;max-width:320px;border-radius:0;transform:translateX(100%);transition:transform var(--transition-base);">
    <div class="modal-header">
      <h2 class="modal-title">Document History</h2>
      <button class="btn btn-ghost btn-icon" onclick="closeModal('versions-drawer')">✕</button>
    </div>
    <div class="modal-body" id="versions-list-body" style="padding:0;">
      
    </div>
  </div>
</div>

<div class="ai-chat-bubble">
  <button class="ai-chat-btn" onclick="toggleAIChat()" style="display:flex;align-items:center;justify-content:center;"><i data-lucide="bot" style="width:24px;height:24px;"></i></button>
  <div class="ai-chat-window" id="ai-chat-window">
    <div class="ai-chat-header">
      <span><i data-lucide="bot" style="width:16px;height:16px;display:inline-block;vertical-align:middle;margin-right:6px;"></i>CitationGuard AI Assistant</span>
      <button class="btn btn-ghost btn-icon-sm" style="color:#fff;margin-left:auto;" onclick="toggleAIChat()">✕</button>
    </div>
    <div class="ai-chat-messages" id="ai-chat-messages">
      <div class="ai-msg assistant">Hello! I am your Academic Integrity advisor. How can I help verify your citations or research integrity today?</div>
    </div>
    <div class="ai-chat-input">
      <input type="text" id="ai-chat-input-field" placeholder="Ask a citation question..." onkeydown="if(event.key==='Enter') sendChatMessage()">
      <button class="btn btn-primary btn-sm" onclick="sendChatMessage()">Send</button>
    </div>
  </div>
</div>

<div class="modal-overlay" id="add-citation-modal">
  <div class="modal modal-lg">
    <div class="modal-header">
      <h2 class="modal-title">Insert Reference Citation</h2>
      <button class="btn btn-ghost btn-icon" onclick="closeModal('add-citation-modal')">✕</button>
    </div>
    <div class="modal-body">
      <div class="form-group">
        <label class="form-label" for="cit-title">Source Title *</label>
        <input type="text" id="cit-title" name="cit-title" class="input" placeholder="e.g. DNA double-strand breaks induced by CRISPR-Cas9" autocomplete="off">
      </div>
      <div class="grid-2" style="gap:1rem;">
        <div class="form-group" style="margin:0;">
          <label class="form-label" for="cit-authors">Authors *</label>
          <input type="text" id="cit-authors" name="cit-authors" class="input" placeholder="e.g. Chen, S., Robertson, J." autocomplete="off">
        </div>
        <div class="form-group" style="margin:0;">
          <label class="form-label" for="cit-year">Year *</label>
          <input type="text" id="cit-year" name="cit-year" class="input" placeholder="e.g. 2024" autocomplete="off">
        </div>
      </div>
      <div class="grid-2" style="gap:1rem;margin-top:1rem;">
        <div class="form-group" style="margin:0;">
          <label class="form-label" for="cit-journal">Journal / Book Title</label>
          <input type="text" id="cit-journal" name="cit-journal" class="input" placeholder="e.g. Nature Biotech" autocomplete="off">
        </div>
        <div class="form-group" style="margin:0;">
          <label class="form-label" for="cit-doi">DOI</label>
          <input type="text" id="cit-doi" name="cit-doi" class="input" placeholder="e.g. 10.1038/nbt.3123" autocomplete="off">
        </div>
      </div>
      <div class="grid-2" style="gap:1rem;margin-top:1rem;">
        <div class="form-group" style="margin:0;">
          <label class="form-label" for="cit-pages">Page Numbers</label>
          <input type="text" id="cit-pages" name="cit-pages" class="input" placeholder="e.g. 45-52" autocomplete="off">
        </div>
        <div class="form-group" style="margin:0;">
          <label class="form-label" for="cit-type">Source Type</label>
          <select id="cit-type" name="cit-type" class="select input">
            <option value="journal">Journal Paper</option>
            <option value="book">Book</option>
            <option value="conference">Conference Proceeding</option>
            <option value="website">Website</option>
          </select>
        </div>
      </div>
    </div>
    <div class="modal-footer">
      <button class="btn btn-secondary" onclick="closeModal('add-citation-modal')">Cancel</button>
      <button class="btn btn-primary" onclick="submitCitation()">Insert Citation</button>
    </div>
  </div>
</div>

// Initialize workspace
async function initWorkspace() {
  if (!await authGuard()) return;

const params = new URLSearchParams(location.search);
  currentProjectId = parseInt(params.get('project'));
  
  if (!currentProjectId) {
    showToast('Project ID required. Redirecting to Dashboard...', 'error');
    setTimeout(() => window.location.href = 'dashboard.php', 1500);
    return;
  }

// Load project details
  const projRes = await api.getProject(currentProjectId).catch(() => null);
  if (projRes?.status === 'success') {
    const proj = projRes.data.project;
    document.getElementById('workspace-project-title').textContent = proj.title;
    document.getElementById('workspace-style-select').value = proj.citation_style || 'APA';
    document.getElementById('status-style').textContent = proj.citation_style || 'APA';
    
    // Fetch and store library papers in window for local similarity check reference
    const libRes = await api.getLibraryPapers({ project_id: currentProjectId }).catch(() => null);
    if (libRes?.status === 'success') {
      window.libraryPapers = libRes.data.papers || [];
    }

// Load documents
    const docRes = await api.getDocuments(currentProjectId).catch(() => null);
    if (docRes?.status === 'success') {
      renderDocumentsSidebar(docRes.data.documents);
      if (docRes.data.documents.length > 0) {
        loadDocument(docRes.data.documents[0].id);
      } else {
        createNewDocument();
      }
    }
  }
}

async function loadDocument(docId) {
  currentDocumentId = docId;
  
  // Re-highlight active side menu
  document.querySelectorAll('.doc-item').forEach(el => el.classList.remove('active'));
  
  const docRes = await api.getDocument(docId).catch(() => null);
  if (docRes?.status === 'success') {
    const doc = docRes.data.document;
    currentCitations = doc.citations || [];

// Initialize editor if not done yet
    if (!academicEditor) {
      academicEditor = new AcademicEditor('editor-content', 'editor-toolbar', 'editor-info-bar', {
        onInput: (html) => handleEditorInput(html),
        onSelection: (text) => handleEditorSelection(text)
      });
      citationEngine = new CitationEngine(academicEditor, {
        onAnalysisCompleted: (stats) => handleAnalysisFinished(stats)
      });
    }

academicEditor.setContent(doc.content || '<p></p>');
    // Update word/char count immediately after content is set
    setTimeout(updateWordCount, 50);
    document.getElementById('status-coverage-score').textContent = parseFloat(doc.citation_coverage_score || 0).toFixed(0) + '%';
    const savedPlag = parseFloat(doc.plagiarism_risk_score || 0).toFixed(0);
    document.getElementById('status-risk-score').textContent = savedPlag + '%';
    document.getElementById('similarity-score-text').textContent = savedPlag + '%';
    const plagRisk = savedPlag >= 70 ? 'critical' : (savedPlag >= 40 ? 'high' : (savedPlag >= 20 ? 'moderate' : 'low'));
    document.getElementById('similarity-overall-badge').className = `badge risk-${plagRisk}`;
    document.getElementById('similarity-overall-badge').textContent = plagRisk.toUpperCase();

// Fetch alerts
    loadAlerts();
    loadDNAProfile();
  }
}

async function createNewDocument() {
  const res = await api.createDocument({
    project_id: currentProjectId,
    title: 'Untitled Draft',
    content: '<h1>New Section Title</h1><p>Start your scientific research paragraphs here...</p>'
  }).catch(() => null);
  
  if (res?.status === 'success') {
    showToast('New draft document created!', 'success');
    const docRes = await api.getDocuments(currentProjectId).catch(() => null);
    if (docRes?.status === 'success') {
      renderDocumentsSidebar(docRes.data.documents);
    }
    loadDocument(res.data.document.id);
  }
}

function updateWordCount() {
  const editorEl = document.getElementById('editor-content');
  const rawText  = editorEl ? (editorEl.innerText || '') : '';
  const words    = rawText.trim() === '' ? 0 : rawText.trim().split(/\s+/).length;
  const chars    = rawText.replace(/\s/g, '').length;
  document.querySelector('.word-count').textContent = words.toLocaleString() + ' words';
  document.querySelector('.char-count').textContent = chars.toLocaleString() + ' characters';
}

function handleEditorInput(html) {
  clearTimeout(this.autoSaveTimer);
  document.getElementById('save-indicator').className = 'save-indicator saving';
  document.getElementById('live-analysis-label').textContent = 'Saving draft...';

// Live word/char count on every keystroke
  updateWordCount();

this.autoSaveTimer = setTimeout(async () => {
    await api.saveDocument(currentDocumentId, {
      content: html,
      citation_count: currentCitations.length,
      citation_coverage_score: parseFloat(document.getElementById('status-coverage-score').textContent),
      plagiarism_risk_score: parseFloat(document.getElementById('status-risk-score').textContent)
    }).catch(() => null);

document.getElementById('save-indicator').className = 'save-indicator saved';
    document.getElementById('live-analysis-label').textContent = 'Writing protected by AI';

citationEngine.analyzeDocument(currentDocumentId);
  }, 2000);
}

function handleEditorSelection(text) {
  selectedSentenceText = text;
  if (text.length > 15) {
    searchSources(text);
    checkSimilarity(text);
  }
}

async function triggerFullAnalysis() {
  if (!citationEngine) return;
  showToast('Running full document integrity scan...', 'info');
  await citationEngine.analyzeDocument(currentDocumentId);
  await scanEntireDocSimilarity();
  loadAlerts();
  showToast('Integrity check completed successfully', 'success');
}

async function loadAlerts() {
  const res = await api.getAnalysis(currentDocumentId).catch(() => null);
  const list = document.getElementById('alerts-list');
  const countEl = document.getElementById('alerts-count');

if (res?.status === 'success' && res.data.analysis.length > 0) {
    const listHtml = res.data.analysis.map(a => `
      <div class="alert-card warning" id="alert-card-${a.id}">
        <div class="alert-card-header">
          <span class="badge risk-${a.risk_level}">${a.risk_level.toUpperCase()} ALERT</span>
          <span class="text-xs text-muted">${(a.confidence * 100).toFixed(0)}% confidence</span>
        </div>
        <div class="alert-card-body">
          <div class="alert-card-excerpt">${a.sentence_text}</div>
          <div class="alert-card-reason">${a.ai_response || 'Uncited claims detected. Supporting research references required.'}</div>
          <div class="alert-card-actions">
            <button class="btn btn-primary btn-sm" style="flex:1" onclick="openCitationModal('${a.sentence_text.replace(/'/g, "\\'")}')">Add Citation</button>
            <button class="btn btn-ghost btn-sm" onclick="dismissAlert(${a.id}, this)">Ignore</button>
          </div>
        </div>
      </div>
    `).join('');
    list.innerHTML = listHtml;
    countEl.textContent = res.data.analysis.length;
    countEl.style.display = 'inline-block';
  } else {
    list.innerHTML = `
      <div class="empty-state">
        <div class="empty-icon"><i data-lucide="check" style="width:24px;height:24px;color:var(--success-500);"></i></div>
        <div class="empty-title">All Statements Cited</div>
        <div class="empty-desc">No missing citation warnings detected in the current text scope.</div>
      </div>`;
    countEl.style.display = 'none';
    if (typeof lucide !== 'undefined') {
      lucide.createIcons();
    }
  }
}

async function dismissAlert(alertId, btnEl) {
  if (btnEl) { btnEl.disabled = true; btnEl.textContent = 'Ignoring...'; }
  const res = await api.request('analysis.php', { action: 'dismiss', id: alertId }).catch(() => null);
  const card = document.getElementById(`alert-card-${alertId}`);
  if (card) {
    card.style.opacity = '0';
    card.style.transition = 'opacity 0.3s';
    setTimeout(() => {
      card.remove();
      // Update count badge
      const remaining = document.querySelectorAll('.alert-card').length;
      const countEl = document.getElementById('alerts-count');
      if (remaining === 0) {
        document.getElementById('alerts-list').innerHTML = `
          <div class="empty-state">
            <div class="empty-icon"><i data-lucide="check" style="width:24px;height:24px;color:var(--success-500);"></i></div>
            <div class="empty-title">All Statements Cited</div>
            <div class="empty-desc">No missing citation warnings detected.</div>
          </div>`;
        countEl.style.display = 'none';
        if (typeof lucide !== 'undefined') {
          lucide.createIcons();
        }
      } else {
        countEl.textContent = remaining;
      }
    }, 300);
  }
  showToast('Alert dismissed', 'info');
}

async function loadDNAProfile() {
  if (!academicEditor || !citationEngine) return;
  const sentences = citationEngine.getSentences ? citationEngine.getSentences() : [];
  if (sentences.length === 0) return;

// Build a simple local DNA profile without AI call
  const totalSents = sentences.length;
  const citedSents = sentences.filter(s => s.hasCitation).length;
  const coverage   = totalSents > 0 ? Math.round((citedSents / totalSents) * 100) : 95;

document.getElementById('dna-overall-score').textContent = `${coverage}%`;
  document.getElementById('dna-overall-score').style.color = coverage >= 80 ? 'var(--success-600)' : (coverage >= 50 ? 'var(--warning-600)' : 'var(--danger-600)');
  document.getElementById('dna-profile-type').textContent = coverage >= 80 ? 'INTEGRAL SOURCE ALIGNMENT' : (coverage >= 50 ? 'PARTIAL SOURCE ALIGNMENT' : 'WEAK SOURCE ALIGNMENT');

let currentSearchResults = [];

async function searchSources(q) {
  if (!q || !q.trim()) return;
  updateGoogleScholarLink();
  
  const resList = document.getElementById('suggestions-list');
  resList.innerHTML = `<div class="text-center py-4"><span class="spinner"></span></div>`;
  
  const index = document.getElementById('source-search-index').value;
  let papers = [];
  
  try {
    if (index === 'local') {
      papers = await aiService.suggestCitations(q);
    } else if (index === 'crossref') {
      papers = await fetchCrossRef(q);
    } else if (index === 'semantic') {
      papers = await fetchSemanticScholar(q);
    } else if (index === 'pubmed') {
      papers = await fetchPubMed(q);
    } else if (index === 'arxiv') {
      papers = await fetchArXiv(q);
    }
  } catch (err) {
    console.error('API Error: ', err);
    resList.innerHTML = `<p class="text-danger text-sm text-center">Failed to fetch results from ${index.toUpperCase()}.</p>`;
    return;
  }
  
  currentSearchResults = papers;
  
  if (papers.length > 0) {
    resList.innerHTML = papers.map((p, i) => {
      return `
        <div class="cite-suggestion" style="margin-bottom:0.75rem;padding:0.75rem;border:1px solid var(--color-border);border-radius:8px;background:#fff;text-align:left;">
          <div class="cite-title" style="font-weight:700;font-size:12px;margin-bottom:4px;color:var(--gray-900);line-height:1.4;">${p.title}</div>
          <div class="cite-authors" style="font-size:11px;color:var(--gray-600);">${p.authors} (${p.year})</div>
          <div class="cite-meta" style="font-size:10px;color:var(--gray-500);margin-top:2px;">
            <span>Journal: ${p.journal || 'Research Proceedings'}</span>
          </div>
          ${p.doi ? `<div class="cite-doi" style="font-size:10px;color:var(--primary-600);margin-top:2px;font-family:monospace;word-break:break-all;">DOI: ${p.doi}</div>` : ''}
          <div style="display:flex;gap:0.25rem;margin-top:0.5rem;">
            <button class="btn btn-primary btn-sm" style="font-size:10px;padding:2px 6px;flex:1;" onclick="insertSuggestedCitationFromIndex(${i})">Insert [Cit]</button>
            ${index !== 'local' ? `<button class="btn btn-secondary btn-sm" id="import-btn-${i}" style="font-size:10px;padding:2px 6px;" onclick="importToLibraryFromIndex(${i}, this)">Import</button>` : ''}
          </div>
        </div>
      `;
    }).join('');
  } else {
    resList.innerHTML = `<p class="text-muted text-sm text-center">No reference citations found for the query.</p>`;
  }
}

function insertSuggestedCitationFromIndex(idx) {
  const p = currentSearchResults[idx];
  if (!p) return;
  insertSuggestedCitation(p.authors, p.year, p.title, p.journal || '', p.doi || '');
}

async function importToLibraryFromIndex(idx, btnEl) {
  const p = currentSearchResults[idx];
  if (!p) return;
  
  btnEl.disabled = true;
  btnEl.textContent = 'Importing...';
  
  const res = await api.importPaperMetadata({
    project_id: currentProjectId,
    title: p.title,
    authors: p.authors,
    year: p.year,
    journal: p.journal || 'Research Proceedings',
    doi: p.doi || '',
    abstract: p.abstract || ''
  }).catch(() => null);
  
  if (res?.status === 'success') {
    btnEl.textContent = 'Imported';
    btnEl.className = 'btn btn-success btn-sm';
    btnEl.disabled = true;
    showToast('Reference imported into your project library!', 'success');
    
    // Refresh library papers loaded in workspace state
    const libRes = await api.getLibraryPapers({ project_id: currentProjectId }).catch(() => null);
    if (libRes?.status === 'success') {
      window.libraryPapers = libRes.data.papers || [];
    }
  } else {
    btnEl.disabled = false;
    btnEl.textContent = 'Import';
    showToast(res?.message || 'Failed to import reference', 'error');
  }
}

async function fetchCrossRef(q) {
  const url = `https://api.crossref.org/works?query=${encodeURIComponent(q)}&rows=10`;
  const res = await fetch(url).then(r => r.json());
  const items = res?.message?.items || [];
  return items.map(item => {
    let authors = 'Unknown Authors';
    if (item.author) {
      authors = item.author.map(a => {
        if (a.family && a.given) return `${a.family}, ${a.given}`;
        return a.family || a.name || 'Unknown';
      }).join(', ');
    }
    let year = 'n.d.';
    if (item.issued && item.issued['date-parts'] && item.issued['date-parts'][0]) {
      year = item.issued['date-parts'][0][0];
    } else if (item.created && item.created['date-parts'] && item.created['date-parts'][0]) {
      year = item.created['date-parts'][0][0];
    }
    return {
      title: item.title?.[0] || 'Untitled',
      authors: authors,
      year: String(year),
      journal: item['container-title']?.[0] || 'CrossRef Index',
      doi: item.DOI || '',
      abstract: ''
    };
  });
}

async function fetchSemanticScholar(q) {
  const url = `https://api.semanticscholar.org/graph/v1/paper/search?query=${encodeURIComponent(q)}&limit=10&fields=title,authors,year,venue,externalIds,abstract`;
  const res = await fetch(url).then(r => r.json());
  const items = res?.data || [];
  return items.map(item => {
    const authors = item.authors ? item.authors.map(a => a.name).join(', ') : 'Unknown Authors';
    return {
      title: item.title || 'Untitled',
      authors: authors,
      year: String(item.year || 'n.d.'),
      journal: item.venue || 'Semantic Scholar',
      doi: item.externalIds?.DOI || '',
      abstract: item.abstract || ''
    };
  });
}

async function fetchPubMed(q) {
  const searchUrl = `https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=${encodeURIComponent(q)}&retmode=json&retmax=10`;
  const searchRes = await fetch(searchUrl).then(r => r.json());
  const ids = searchRes?.esearchresult?.idlist || [];
  if (ids.length === 0) return [];
  
  const summaryUrl = `https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&id=${ids.join(',')}&retmode=json`;
  const summaryRes = await fetch(summaryUrl).then(r => r.json());
  const results = summaryRes?.result || {};
  
  return ids.map(id => {
    const item = results[id] || {};
    const authors = item.authors ? item.authors.map(a => a.name).join(', ') : 'Unknown Authors';
    const year = item.pubdate ? item.pubdate.substring(0, 4) : 'n.d.';
    return {
      title: item.title || 'Untitled',
      authors: authors,
      year: year,
      journal: item.source || 'PubMed Central',
      doi: item.articleids?.find(aid => aid.idtype === 'doi')?.value || '',
      abstract: ''
    };
  });
}

async function fetchArXiv(q) {
  const url = `https://export.arxiv.org/api/query?search_query=all:${encodeURIComponent(q)}&max_results=10`;
  const text = await fetch(url).then(r => r.text());
  const parser = new DOMParser();
  const xmlDoc = parser.parseFromString(text, 'text/xml');
  const entries = xmlDoc.getElementsByTagName('entry');
  const results = [];
  
  for (let i = 0; i < entries.length; i++) {
    const entry = entries[i];
    const title = entry.getElementsByTagName('title')[0]?.textContent?.replace(/\n/g, ' ').trim() || 'Untitled';
    
    const authorsList = [];
    const authorNodes = entry.getElementsByTagName('author');
    for (let j = 0; j < authorNodes.length; j++) {
      authorsList.push(authorNodes[j].getElementsByTagName('name')[0]?.textContent || '');
    }
    
    const published = entry.getElementsByTagName('published')[0]?.textContent || 'n.d.';
    const year = published.substring(0, 4);
    const arxivId = entry.getElementsByTagName('id')[0]?.textContent || '';
    const summary = entry.getElementsByTagName('summary')[0]?.textContent?.trim() || '';
    
    results.push({
      title: title,
      authors: authorsList.join(', '),
      year: year,
      journal: 'arXiv Preprint',
      doi: arxivId.split('/abs/')[1] || arxivId,
      abstract: summary
    });
  }
  return results;
}

async function checkSimilarity(text) {
  const list = document.getElementById('similarity-list');
  list.innerHTML = `<div class="text-center py-4"><span class="spinner"></span><p class="text-xs text-muted" style="margin-top:.5rem;">Checking CrossRef · Semantic Scholar · arXiv...</p></div>`;

const res = await api.checkPlagiarism(text).catch(() => null);
  if (!res || res.status !== 'success') {
    list.innerHTML = `<p class="text-muted text-sm text-center">Plagiarism check unavailable. Please try again.</p>`;
    return;
  }

const d = res.data;
  document.getElementById('similarity-score-text').textContent = `${d.similarityScore}%`;
  document.getElementById('similarity-overall-badge').className = `badge risk-${d.riskLevel}`;
  document.getElementById('similarity-overall-badge').textContent = d.riskLevel.toUpperCase();

const sourceBadge = s => ({ CrossRef:'badge-blue', 'Semantic Scholar':'badge-purple', PubMed:'badge-green', arXiv:'badge-secondary' }[s] || 'badge-secondary');

if (d.similarityScore >= 15) {
    list.innerHTML = `
      <div class="alert alert-danger" style="border-left:4px solid var(--danger-600);background:#FEF2F2;color:#991B1B;padding:.75rem;border-radius:6px;font-size:12px;line-height:1.4;margin-bottom:.75rem;">
        <div class="font-semibold" style="font-weight:700;margin-bottom:4px;">Paraphrasing Risk Detected</div>
        <div>${d.recommendation}</div>
      </div>
      <button class="btn btn-gradient btn-sm" style="width:100%;margin-bottom:.75rem;font-size:11px;display:inline-flex;align-items:center;justify-content:center;gap:6px;" onclick="openRephraseModal(selectedSentenceText || '${text.replace(/'/g,"\\'").substring(0,300)}')"><i data-lucide="sparkles" style="width:12px;height:12px;"></i> Rephrase with AI &rarr; Natural Language</button>
      ${matchCards || '<p class="text-muted text-xs text-center">No specific paper matches returned.</p>'}
      <p class="text-xs text-muted" style="margin-top:.5rem;text-align:right;">Checked: ${(d.sourcesChecked||[]).join(' · ')}</p>`;
  } else {
    list.innerHTML = `<p class="text-success text-sm text-center" style="display:flex;align-items:center;justify-content:center;gap:6px;"><i data-lucide="check" style="width:14px;height:14px;"></i> Low plagiarism risk across all academic databases.</p>
      <p class="text-xs text-muted" style="text-align:center;margin-top:.25rem;">Checked: ${(d.sourcesChecked||[]).join(' · ')}</p>`;
  }
  if (typeof lucide !== 'undefined') {
    lucide.createIcons();
  }
}

async function scanEntireDocSimilarity() {
  const list = document.getElementById('similarity-list');
  list.innerHTML = `<div class="text-center py-4"><span class="spinner"></span><p class="text-xs text-muted" style="margin-top:.5rem;">Scanning CrossRef · Semantic Scholar · arXiv...</p></div>`;

const plainText = academicEditor ? (academicEditor.editor.innerText || '') : '';
  if (plainText.trim().length < 15) {
    showToast('Document text is too short to run plagiarism scan', 'warning');
    list.innerHTML = `<p class="text-muted text-sm text-center">Write more text to run a scan.</p>`;
    return;
  }

if (!res || res.status !== 'success') {
    list.innerHTML = `<p class="text-muted text-sm text-center">Plagiarism check unavailable. Please try again.</p>`;
    return;
  }

await api.saveDocument(currentDocumentId, {
    content: academicEditor.getContent(),
    citation_count: currentCitations.length,
    citation_coverage_score: parseFloat(document.getElementById('status-coverage-score').textContent),
    plagiarism_risk_score: parseFloat(d.similarityScore)
  }).catch(() => null);

const sourceBadge = s => ({ CrossRef:'badge-blue', 'Semantic Scholar':'badge-purple', PubMed:'badge-green', arXiv:'badge-secondary' }[s] || 'badge-secondary');

if (d.similarityScore >= 15) {
    list.innerHTML = `
      <div class="alert alert-danger" style="border-left:4px solid var(--danger-600);background:#FEF2F2;color:#991B1B;padding:.75rem;border-radius:6px;font-size:12px;line-height:1.4;text-align:left;margin-bottom:.75rem;">
        <div style="font-weight:700;margin-bottom:4px;font-size:13px;">High Plagiarism Match Detected!</div>
        <div style="margin-bottom:6px;">${d.recommendation}</div>
        ${d.patterns.length > 0 ? `<div style="font-size:10px;color:var(--danger-700);">Pattern: ${d.patterns.join(', ')}</div>` : ''}
      </div>
      <button class="btn btn-gradient btn-sm" style="width:100%;margin-bottom:.75rem;font-size:11px;display:inline-flex;align-items:center;justify-content:center;gap:6px;" onclick="openRephraseModal(selectedSentenceText || (academicEditor ? academicEditor.editor.innerText.substring(0,800) : ''))"><i data-lucide="sparkles" style="width:12px;height:12px;"></i> Rephrase Flagged Text with AI &rarr; Natural Language</button>
      ${matchCards}
      <p class="text-xs text-muted" style="margin-top:.5rem;text-align:right;">Checked: ${(d.sourcesChecked||[]).join(' · ')}</p>`;
    showToast('Plagiarism scan complete — matches found!', 'warning');
  } else {
    list.innerHTML = `
      <p class="text-success text-sm text-center" style="padding:1rem;display:flex;align-items:center;justify-content:center;gap:6px;"><i data-lucide="check" style="width:14px;height:14px;"></i> Low plagiarism risk. No significant matches found.</p>
      <p class="text-xs text-muted" style="text-align:center;">Checked: ${(d.sourcesChecked||[]).join(' · ')}</p>`;
    showToast('Plagiarism scan complete — low risk', 'success');
  }
  if (typeof lucide !== 'undefined') {
    lucide.createIcons();
  }
}

async function checkAIContent() {
  const details = document.getElementById('ai-verify-details');
  details.innerHTML = `<div class="text-center py-4"><span class="spinner"></span><p class="text-xs text-muted" style="margin-top:.5rem;">Analyzing with AI detector...</p></div>`;

if (!academicEditor) {
    details.innerHTML = `<p class="text-muted text-sm text-center">Editor not ready. Please wait.</p>`;
    return;
  }

const text = academicEditor.editor ? (academicEditor.editor.innerText || '') : academicEditor.getContent();
  if (text.trim().length < 20) {
    details.innerHTML = `<p class="text-muted text-sm text-center">Write at least a paragraph to run AI detection.</p>`;
    return;
  }

// Heuristic AI detection (no external API needed)
  const sentences = text.match(/[^.!?]+[.!?]+/g) || [];
  const avgLen    = sentences.reduce((s, x) => s + x.trim().split(/\s+/).length, 0) / (sentences.length || 1);
  const passive   = (text.match(/\b(is|are|was|were|been|being)\s+\w+ed\b/gi) || []).length;
  const hedges    = (text.match(/\b(however|furthermore|nevertheless|moreover|additionally|consequently|therefore)\b/gi) || []).length;
  const aiScore   = Math.min(95, Math.round(((avgLen > 22 ? 30 : 0) + (passive > 5 ? 20 : 0) + (hedges > 4 ? 25 : 0) + Math.random() * 15)));
  const verified  = 100 - aiScore;

document.getElementById('ai-verify-score').textContent  = `${verified}/100`;
  document.getElementById('ai-content-score').textContent = `${aiScore}%`;

details.innerHTML = `
    <div style="margin-top:.75rem;padding:.75rem;border-radius:8px;border:1px solid var(--color-border);">
      <div style="font-weight:700;font-size:12px;color:${color};margin-bottom:.5rem;">${label}</div>
      ${indicators.map(i => `<div class="text-xs text-muted" style="margin-bottom:.35rem;">⚠ ${i}</div>`).join('')}
      <p class="text-xs text-muted" style="margin-top:.5rem;border-top:1px solid var(--color-border-subtle);padding-top:.5rem;">AI detection is probabilistic. Results are indicative, not definitive.</p>
    </div>`;
}

function handleAnalysisFinished(stats) {
  document.getElementById('status-coverage-score').textContent = stats.coverageScore.toFixed(0) + '%';
  document.getElementById('status-risk-score').textContent = stats.plagiarismRisk.toFixed(0) + '%';
}

function openCitationModal(sentenceText) {
  selectedSentenceText = sentenceText;
  openModal('add-citation-modal');
}

async function submitCitation() {
  const title = document.getElementById('cit-title').value.trim();
  const authors = document.getElementById('cit-authors').value.trim();
  const year = document.getElementById('cit-year').value.trim();
  if (!title || !authors || !year) {
    showToast('Please fill all required fields', 'error');
    return;
  }
  
  const citationKey = `cit_${Date.now()}`;
  const res = await api.addCitation({
    document_id: currentDocumentId,
    source_title: title,
    authors: authors,
    year: year,
    journal: document.getElementById('cit-journal').value,
    doi: document.getElementById('cit-doi').value,
    page_numbers: document.getElementById('cit-pages').value,
    source_type: document.getElementById('cit-type').value,
    citation_key: citationKey,
    citation_style: document.getElementById('workspace-style-select').value
  }).catch(() => null);
  
  if (res?.status === 'success') {
    closeModal('add-citation-modal');
    showToast('Citation added successfully!', 'success');
    
    const index = currentCitations.length + 1;
    academicEditor.insertCitation(`[${index}]`, res.data.citation.id);
    
    currentCitations.push(res.data.citation);
    loadAlerts();
  }
}

function insertSuggestedCitation(authors, year, title, journal, doi) {
  document.getElementById('cit-title').value = title;
  document.getElementById('cit-authors').value = authors;
  document.getElementById('cit-year').value = year;
  document.getElementById('cit-journal').value = journal;
  document.getElementById('cit-doi').value = doi;
  openModal('add-citation-modal');
}

// ── AI Chat ──────────────────────────────────────────────────
function toggleAIChat() {
  document.getElementById('ai-chat-window').classList.toggle('open');
}

async function sendChatMessage() {
  const input = document.getElementById('ai-chat-input-field');
  const msgText = input.value.trim();
  if (!msgText) return;
  
  input.value = '';
  const chatMsgs = document.getElementById('ai-chat-messages');
  
  const userDiv = document.createElement('div');
  userDiv.className = 'ai-msg user animate-fade-in-up';
  userDiv.textContent = msgText;
  chatMsgs.appendChild(userDiv);
  chatMsgs.scrollTop = chatMsgs.scrollHeight;
  
  const assistantDiv = document.createElement('div');
  assistantDiv.className = 'ai-msg assistant animate-fade-in-up';
  assistantDiv.innerHTML = `<span class="thinking-dots"><span></span><span></span><span></span></span>`;
  chatMsgs.appendChild(assistantDiv);
  chatMsgs.scrollTop = chatMsgs.scrollHeight;
  
  const context = academicEditor ? academicEditor.getContent() : '';
  const response = await aiService.chat(msgText, context);
  assistantDiv.innerHTML = response;
  chatMsgs.scrollTop = chatMsgs.scrollHeight;
}

// ── Version history drawer ────────────────────────────────────
async function openVersionsDrawer() {
  openModal('versions-drawer');
  const res = await api.getVersions(currentDocumentId).catch(() => null);
  const listBody = document.getElementById('versions-list-body');
  
  if (res?.status === 'success' && res.data.versions.length > 0) {
    listBody.innerHTML = res.data.versions.map(v => `
      <div class="version-item" onclick="restoreVersion(${v.id})">
        <div class="version-number">Version ${v.version_number}</div>
        <div class="version-date">${formatDate(v.created_at)} · ${v.word_count} words</div>
        <div class="version-summary">${v.change_summary || 'Auto-save version'}</div>
      </div>
    `).join('');
  } else {
    listBody.innerHTML = `<p class="text-muted text-sm text-center py-8">No past versions found.</p>`;
  }
}

async function restoreVersion(versionId) {
  if (!confirm("Are you sure you want to restore this version? Your current unsaved content will be overwritten.")) return;
  const res = await api.restoreVersion(currentDocumentId, versionId).catch(() => null);
  if (res?.status === 'success') {
    academicEditor.setContent(res.data.content);
    closeModal('versions-drawer');
    showToast('Version restored successfully', 'success');
  }
}

// ── AI Rephrasing ─────────────────────────────────────────────
let _rephraseOriginal = '';
let _savedSelection   = null;

function openRephraseModal(text) {
  if (!text || !text.trim()) {
    showToast('Highlight the plagiarised text in the editor first, then click Rephrase.', 'warning');
    return;
  }
  _rephraseOriginal = text.trim();
  // Save current editor selection so we can restore it for Apply
  const sel = window.getSelection();
  _savedSelection = (sel && sel.rangeCount > 0) ? sel.getRangeAt(0).cloneRange() : null;

document.getElementById('rephrase-original-text').textContent = _rephraseOriginal;
  document.getElementById('rephrase-output').innerHTML = '';
  document.getElementById('rephrase-apply-btn').style.display = 'none';
  document.getElementById('rephrase-copy-btn').style.display  = 'none';
  openModal('rephrase-modal');
  rephraseWithAI(_rephraseOriginal);
}

async function rephraseWithAI(text) {
  const out  = document.getElementById('rephrase-output');
  const applyBtn = document.getElementById('rephrase-apply-btn');
  const copyBtn  = document.getElementById('rephrase-copy-btn');

out.innerHTML = `<div class="text-center py-3"><span class="spinner"></span><p class="text-xs text-muted" style="margin-top:.5rem;">Rephrasing in natural human language...</p></div>`;

const prompt = `You are an expert academic writer. Rephrase the following text so it sounds naturally written by a human researcher — conversational yet scholarly, avoiding overly formal or robotic phrasing. Preserve all factual content and technical accuracy. Return ONLY the rephrased text with no explanations, quotes, or preamble.\n\nText to rephrase:\n${text}`;

const res = await fetch('api/ai_proxy.php', {
    method: 'POST',
    headers: { 'Content-Type': 'application/json' },
    body: JSON.stringify({ prompt })
  }).then(r => r.json()).catch(() => null);

const rephrased = res?.content?.trim() || res?.choices?.[0]?.message?.content?.trim() || '';

if (!rephrased) {
    out.innerHTML = `<p class="text-danger text-sm text-center">AI rephrasing failed. Please try again.</p>`;
    return;
  }

out.innerHTML = `
    <div style="background:linear-gradient(135deg,#F0FDF4,#ECFDF5);border:1px solid var(--success-300,#6ee7b7);border-radius:8px;padding:.9rem;font-size:13px;line-height:1.7;color:var(--gray-800);white-space:pre-wrap;">${rephrased.replace(/</g,'&lt;').replace(/>/g,'&gt;')}</div>`;

applyBtn.dataset.rephrased = rephrased;
  applyBtn.style.display = 'inline-flex';
  copyBtn.dataset.rephrased  = rephrased;
  copyBtn.style.display  = 'inline-flex';
}

function applyRephrasedText(btn) {
  const rephrased = btn.dataset.rephrased;
  if (!rephrased || !academicEditor) return;

const editor = academicEditor.editor;
  if (!editor) return;

editor.focus();

// Helper to format plain text / linebreaks into HTML paragraphs
  const formatAsHTML = (txt) => {
    const lines = txt.split(/\n\s*\n/).map(s => s.trim()).filter(Boolean);
    if (lines.length > 1) {
      return lines.map(l => `<p>${l}</p>`).join('');
    }
    return txt.replace(/\n/g, '<br>');
  };

// Strategy 1: If _savedSelection was recorded and is valid
  if (_savedSelection) {
    try {
      const sel = window.getSelection();
      sel.removeAllRanges();
      sel.addRange(_savedSelection);

if (!_savedSelection.collapsed) {
        const formatted = formatAsHTML(rephrased);
        if (!document.execCommand('insertHTML', false, formatted)) {
          const range = sel.getRangeAt(0);
          range.deleteContents();
          const temp = document.createElement('div');
          temp.innerHTML = formatted;
          const frag = document.createDocumentFragment();
          while (temp.firstChild) frag.appendChild(temp.firstChild);
          range.insertNode(frag);
        }
        _savedSelection = null;
        closeModal('rephrase-modal');
        showToast('Rephrased text applied to editor!', 'success');
        academicEditor.handleInput();
        return;
      }
    } catch(e) {}
  }

// Strategy 2: Block & DOM Node Matching Strategy
  const orig = (_rephraseOriginal || '').trim();
  const cleanOrig = orig.replace(/\s+/g, ' ');

if (cleanOrig && editor) {
    const blocks = Array.from(editor.querySelectorAll('p, h1, h2, h3, h4, h5, h6, blockquote, div'));
    
    // Find block elements whose text matches cleanOrig or cleanOrig contains block text
    const matchingBlocks = blocks.filter(b => {
      const bt = b.textContent.trim().replace(/\s+/g, ' ');
      return bt && (cleanOrig.includes(bt) || bt.includes(cleanOrig) || 
        (cleanOrig.length > 20 && bt.length > 20 && (cleanOrig.startsWith(bt.substring(0, 20)) || bt.startsWith(cleanOrig.substring(0, 20)))));
    });

if (matchingBlocks.length > 0) {
      const formatted = formatAsHTML(rephrased);
      const replacementHTML = formatted.startsWith('<p>') || formatted.startsWith('<h') ? formatted : `<p>${formatted}</p>`;
      
      matchingBlocks[0].outerHTML = replacementHTML;
      
      // Remove any subsequent matching blocks if original text spanned across multiple blocks
      for (let i = 1; i < matchingBlocks.length; i++) {
        if (matchingBlocks[i].parentNode) {
          matchingBlocks[i].parentNode.removeChild(matchingBlocks[i]);
        }
      }
      
      closeModal('rephrase-modal');
      showToast('Rephrased text applied to editor!', 'success');
      academicEditor.handleInput();
      return;
    }

// Substring word match fallback across paragraphs
    const words = cleanOrig.split(' ').filter(w => w.length > 3);
    if (words.length > 0) {
      let bestBlock = null;
      let maxScore = 0;
      
      blocks.forEach(b => {
        const bt = b.textContent.toLowerCase();
        let score = 0;
        words.forEach(w => { if (bt.includes(w.toLowerCase())) score++; });
        if (score > maxScore && score >= Math.min(2, words.length)) {
          maxScore = score;
          bestBlock = b;
        }
      });

if (bestBlock) {
        const formatted = formatAsHTML(rephrased);
        const replacementHTML = formatted.startsWith('<p>') || formatted.startsWith('<h') ? formatted : `<p>${formatted}</p>`;
        bestBlock.outerHTML = replacementHTML;
        closeModal('rephrase-modal');
        showToast('Rephrased text applied to editor!', 'success');
        academicEditor.handleInput();
        return;
      }
    }
  }

// Strategy 3: Fallback editor content replacement
  if (rephrased) {
    const formatted = formatAsHTML(rephrased);
    editor.innerHTML = formatted.startsWith('<p>') || formatted.startsWith('<h') ? formatted : `<p>${formatted}</p>`;
    closeModal('rephrase-modal');
    showToast('Rephrased text applied to editor!', 'success');
    academicEditor.handleInput();
    return;
  }
}

function copyRephrased(btn) {
  const rephrased = btn.dataset.rephrased;
  if (!rephrased) return;
  navigator.clipboard.writeText(rephrased).then(() =>
    showToast('Rephrased text copied to clipboard!', 'success')
  );
}

initWorkspace();
</script>

<div class="modal-overlay" id="rephrase-modal">
  <div class="modal" style="max-width:600px;width:95%;">
    <div class="modal-header" style="background:var(--primary-600);color:#fff;border-radius:12px 12px 0 0;padding:1.1rem 1.5rem;">
      <h2 class="modal-title" style="color:#fff;font-size:1rem;display:flex;align-items:center;gap:6px;"><i data-lucide="sparkles" style="width:16px;height:16px;"></i> AI Rephraser &mdash; Natural Language</h2>
      <button class="btn btn-ghost btn-icon" style="color:#fff;" onclick="closeModal('rephrase-modal')">&#x2715;</button>
    </div>
    <div class="modal-body" style="padding:1.25rem;">
      <div style="margin-bottom:1rem;">
        <div style="font-size:11px;font-weight:700;color:var(--gray-500);text-transform:uppercase;letter-spacing:.06em;margin-bottom:.4rem;">Original (Flagged) Text</div>
        <div id="rephrase-original-text" style="background:#FEF2F2;border:1px solid #FECACA;border-radius:8px;padding:.75rem;font-size:12px;line-height:1.6;color:#991B1B;max-height:160px;overflow-y:auto;white-space:pre-wrap;"></div>
      </div>
      <div style="display:flex;align-items:center;gap:.5rem;margin:1rem 0;">
        <div style="flex:1;height:1px;background:var(--color-border);"></div>
        <span style="font-size:11px;color:var(--gray-400);">AI rephrasing &darr;</span>
        <div style="flex:1;height:1px;background:var(--color-border);"></div>
      </div>
      <div style="margin-bottom:1rem;">
        <div style="font-size:11px;font-weight:700;color:var(--gray-500);text-transform:uppercase;letter-spacing:.06em;margin-bottom:.4rem;">Rephrased in Natural Human Language</div>
        <div id="rephrase-output" style="min-height:80px;"></div>
      </div>
    </div>
    <div class="modal-footer" style="display:flex;gap:.5rem;justify-content:flex-end;padding:1rem 1.25rem;border-top:1px solid var(--color-border);">
      <button class="btn btn-ghost btn-sm" onclick="closeModal('rephrase-modal')">Cancel</button>
      <button id="rephrase-copy-btn" class="btn btn-secondary btn-sm" style="display:none;display:inline-flex;align-items:center;gap:4px;" onclick="copyRephrased(this)"><i data-lucide="copy" style="width:12px;height:12px;"></i> Copy</button>
      <button id="rephrase-apply-btn" class="btn btn-gradient btn-sm" style="display:none;display:inline-flex;align-items:center;gap:4px;" onclick="applyRephrasedText(this)"><i data-lucide="check" style="width:12px;height:12px;"></i> Apply to Document</button>
    </div>
  </div>
</div>

<?php include 'includes/footer.php'; ?>

OnlinePixelz - The Open Source of Knowledge

The Modern Digital Toolbox: How to Handle Everyday File, Image, and Data Tasks Without Software Bloat

August 29, 2026

OmniTools: Fast, Browser-Based Micro-Tools with Zero Server Uploads

Every day, millions of students, developers, job seekers, and office workers hit the same frustrating roadblock: a simple micro-task that...

What 10 Bloggers Wish They Knew Before Going Full-Time

July 23, 2026

The dream of becoming a full-time blogger has never been more attractive. Millions of people imagine replacing a traditional job...

Simple Home Network Setup That Actually Protects Your Family

July 23, 2026

Why Home Network Security Matters More Than Ever Your home Wi-Fi network has become the digital front door of your...

Tax Changes Every Freelancer Needs to Know Before Filing in 2027

July 16, 2026

The freelance economy continues to expand at an incredible pace, bringing millions of professionals into self-employment across industries such as...

What Are the Advantages and Disadvantages of Web 3.0? A Complete Guide (2026)

July 16, 2026

The internet has evolved dramatically over the past three decades. From static websites in the 1990s to social media and...

Best Car Insurance Quotes for Gig Workers 2026

July 14, 2026

Understanding Insurance Needs in the Gig Economy The gig economy has transformed the way millions of people earn income. Whether...

Vibe Coding: The Complete Guide to AI-Powered Software Development in 2026

June 2, 2026

What is Vibe Coding? Vibe coding is a software development approach where developers describe what they want to build in...

YouTube Influencer Marketing Agency: Best Strategies & Tools for Brand Growth in 2026

May 28, 2026

YouTube Influencer Marketing Agency: YouTube has become one of the most powerful platforms for influencer marketing in the world. In...

YouTube Marketing Tools in 2026: 15 Best Tools to Grow Your Channel Faster

May 27, 2026

Modern YouTube marketing tools featured image showing YouTube analytics dashboard, SEO growth chart, AI content tools, keyword research, and top YouTube marketing platforms for channel growth and video optimization in 2026.

YouTube Marketing: YouTube is no longer just a video-sharing platform. In 2026, it has become one of the most powerful...

Best for Shopify SEO Consultant: Why Your Ecommerce Store Needs in 2026

May 25, 2026

Modern Shopify SEO consultant featured image showing Shopify analytics dashboard, SEO growth chart, ecommerce optimization elements, and digital marketing visuals representing Shopify SEO services, organic traffic growth, higher Google rankings, and ecommerce store success in 2026.

Shopify SEO Consultant: Running a Shopify store in 2026 feels a lot like opening a beautiful shop in the middle...